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Exons

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Discerning novel splice junctions derived from RNA-seq alignment: a deep learning approach.

BMC genomics 30591034
BACKGROUND: Exon splicing is a regulated cellular process in the transcription of protein-coding genes. Technological advancements and cost reductions in RNA sequencing have made quantitative and qualitative assessments of the transcriptome both poss...
Deep Learning Exons Gene Expression Profiling Genome, Human Humans RNA Splicing Sequence Alignment Sequence Analysis, RNA Software
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Deep-learning augmented RNA-seq analysis of transcript splicing.

Nature methods 30923373
A major limitation of RNA sequencing (RNA-seq) analysis of alternative splicing is its reliance on high sequencing coverage. We report DARTS (https://github.com/Xinglab/DARTS), a computational framework that integrates deep-learning-based predictions...
Algorithms Alternative Splicing Bayes Theorem Deep Learning Epigenomics Exons Gene Expression Profiling Gene Expression Regulation Hep G2 Cells High-Throughput Nucleotide Sequencing Humans K562 Cells Models, Statistical Reproducibility of Results RNA RNA Splicing Sequence Analysis, RNA Signal Processing, Computer-Assisted
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Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorder.

PLoS computational biology 30973878
Gestational alcohol exposure causes fetal alcohol spectrum disorder (FASD) and is a prominent cause of neurodevelopmental disability. Whole transcriptome sequencing (RNA-Seq) offer insights into mechanisms underlying FASD, but gene-level analysis pro...
Animals Big Data Chick Embryo Cluster Analysis Computational Biology Databases, Nucleic Acid Disease Models, Animal Ethanol Exons Female Fetal Alcohol Spectrum Disorders Gene Expression Profiling Humans MicroRNAs Pregnancy Principal Component Analysis Unsupervised Machine Learning
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DL-CNV: A deep learning method for identifying copy number variations based on next generation target sequencing.

Mathematical biosciences and engineering : MBE 31731347
Copy number variations (CNVs) play an important role in many types of cancer. With the rapid development of next generation sequencing (NGS) techniques, many methods for detecting CNVs of a single sample have emerged: (i) require genome-wide data of ...
Algorithms Area Under Curve Carcinoma, Non-Small-Cell Lung Databases, Factual Deep Learning DNA Copy Number Variations Exons False Positive Reactions Genome-Wide Association Study Genome, Human High-Throughput Nucleotide Sequencing Humans In Situ Hybridization, Fluorescence Lung Neoplasms Proto-Oncogene Proteins c-met Receptor, ErbB-2 Reproducibility of Results ROC Curve Sensitivity and Specificity
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A network-based computational framework to predict and differentiate functions for gene isoforms using exon-level expression data.

Methods (San Diego, Calif.) 32534132
MOTIVATION: Alternative splicing makes significant contributions to functional diversity of transcripts and proteins. Many alternatively spliced gene isoforms have been shown to perform specific biological functions under different contexts. In addit...
Alternative Splicing Computational Biology Exons Gene Expression Regulation High-Throughput Nucleotide Sequencing Humans Neural Networks, Computer Protein Isoforms Sequence Analysis, RNA Software
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Machine learning based CRISPR gRNA design for therapeutic exon skipping.

PLoS computational biology 33417623
Restoring gene function by the induced skipping of deleterious exons has been shown to be effective for treating genetic disorders. However, many of the clinically successful therapies for exon skipping are transient oligonucleotide-based treatments ...
Animals Cells, Cultured CRISPR-Cas Systems Embryonic Stem Cells Exons Gene Editing Gene Library Genetic Therapy Humans Machine Learning Mice RNA, Guide, CRISPR-Cas Systems
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Prediction of Alzheimer's disease-specific phospholipase c gamma-1 SNV by deep learning-based approach for high-throughput screening.

Proceedings of the National Academy of Sciences of the United States of America 33397809
Exon splicing triggered by unpredicted genetic mutation can cause translational variations in neurodegenerative disorders. In this study, we discover Alzheimer's disease (AD)-specific single-nucleotide variants (SNVs) and abnormal exon splicing of ph...
Alzheimer Disease Animals Computer Simulation Deep Learning Disease Models, Animal Exons Genetic Predisposition to Disease Genome-Wide Association Study Genome, Human High-Throughput Screening Assays Humans Mice Phospholipase C gamma Polymorphism, Single Nucleotide RNA Splicing RNA, Messenger
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CADD-Splice-improving genome-wide variant effect prediction using deep learning-derived splice scores.

Genome medicine 33618777
BACKGROUND: Splicing of genomic exons into mRNAs is a critical prerequisite for the accurate synthesis of human proteins. Genetic variants impacting splicing underlie a substantial proportion of genetic disease, but are challenging to identify beyond...
Base Sequence Deep Learning Exons Genetic Variation Genome-Wide Association Study Humans Introns RNA Splicing
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MET Exon 14 Skipping: A Case Study for the Detection of Genetic Variants in Cancer Driver Genes by Deep Learning.

International journal of molecular sciences 33921709
BACKGROUND: Disruption of alternative splicing (AS) is frequently observed in cancer and might represent an important signature for tumor progression and therapy. Exon skipping (ES) represents one of the most frequent AS events, and in non-small cell...
Deep Learning Exons Genetic Variation Humans Neural Networks, Computer
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A deep learning approach to identify gene targets of a therapeutic for human splicing disorders.

Nature communications 34099697
Pre-mRNA splicing is a key controller of human gene expression. Disturbances in splicing due to mutation lead to dysregulated protein expression and contribute to a substantial fraction of human disease. Several classes of splicing modulator compound...
Animals Computational Biology Cystic Fibrosis Transmembrane Conductance Regulator Deep Learning Exons Gene Targeting HEK293 Cells Humans Mice Mice, Transgenic Mutation MutL Protein Homolog 1 Phenethylamines Pyridazines RNA Splicing Sterol Esterase tau Proteins Transcriptome
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